PyAutoGut

PyAutoGut is the Gut of the PyAutoScientist — the organ of elimination. It owns the full lifecycle of condemned self-material: the stale branches, git stash entries, dead code and retired tests that a hygiene sweep is 95%-but-not-100% sure is trash. The Gut holds each item recoverably through a transit window, then performs the final deletion itself.

How PyAutoGut works

1. Condemn. The Brain's hygiene conductor (/hygiene) decides an item is spent and files it in the manifest — the condemned.md ledger in the Mind (symmetric to parked.md: parked will resume, condemned awaits elimination).
2. Transit. Fragile forms (unmerged branches, stashes) are first materialised as real commits and pushed here as durable git refs under refs/heads/archive/condemned/<name> — this repo is the attic remote. Until its sweep-after date, recovery is just a checkout.
3. Void. A batch sweep (/repo_cleanup safety gates against the manifest) eliminates items past their transit window — the Gut deletes; the entry leaves the ledger.

The split mirrors Heart ↔ vitals: the conductor reasons and drives, the organ holds and voids.

The board, and the void button

PyAutoGut Dashboard — a clear overview of everything in the Gut: every ref under refs/heads/archive/condemned/ read against the Mind's condemned.md, in buckets — due (past sweep-after), in transit (days left), held (undated, kept until a human asks), orphan refs (no ledger entry), dangling entries (ref missing), refs held on another repo, history-only entries (archive-ref: n/a) and the recently voided. Rendered by scripts/board.py and published daily and after every void by gut_board.yml, with a state.json feed for the organism cockpit.

Void permanently on a row opens a prefilled issue titled void: <name>; submitting it is the yes. void.yml then deletes that ref, comments the repo and pre-delete SHA, closes the issue and re-renders the board. Void all due does the same for every due row (void: all-due). The button reaches refs held on another repo too (an entry whose archive-ref says … on <Repo> origin): refs in the Gut are deleted with this repo's own token, refs on a sibling repo with the org PAT secrets.PAT_PYAUTOLABS — the token Brain's branch_archive.yml already pushes cross-repo with. The PAT is sent as an HTTP header from an empty scratch repo (never in a URL or a log line, and masked). Without the PAT, or when the PAT cannot reach a repo (a repo born after the PAT was minted may be missing from its repository list), that ref is reported per row in the closing comment — which names the repo — and left in place, and the issue stays open. The contract:

• only owners, members and collaborators can void — anyone else's issue is closed untouched;
• names must sit inside the archive namespace (no .., no main, no globs);
• held (undated) entries — in the Gut or on a sibling repo — are never one-tap voidable and never in all-due; void them in a session with bin/pyauto-gut void <name> --yes;
• refs without a ledger entry are voided one at a time, never in bulk;
• voiding removes the bytes; the ledger row stays in condemned.md until a session retires it (the board lists it with a copyable AI assistant prompt), because the workflow cannot edit the Mind.

Full rationale and boundaries: pyautogut-organ-decision. Operating guidance for agents: AGENTS.md. The organism this repo is the Gut of is described once in PyAutoBrain/ORGANISM.md and documented in full at https://pyautoscientist.readthedocs.io.